Format

Send to:

Choose Destination

MBD4 methyl-CpG binding domain 4, DNA glycosylase [ Homo sapiens (human) ]

Gene ID: 8930, updated on 21-Apr-2019

Summary

Official Symbol
MBD4provided by HGNC
Official Full Name
methyl-CpG binding domain 4, DNA glycosylaseprovided by HGNC
Primary source
HGNC:HGNC:6919
See related
Ensembl:ENSG00000129071 MIM:603574
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
MED1
Summary
The protein encoded by this gene is a member of a family of nuclear proteins related by the presence of a methyl-CpG binding domain (MBD). These proteins are capable of binding specifically to methylated DNA, and some members can also repress transcription from methylated gene promoters. This protein contains an MBD domain at the N-terminus that functions both in binding to methylated DNA and in protein interactions and a C-terminal mismatch-specific glycosylase domain that is involved in DNA repair. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Jan 2013]
Expression
Ubiquitous expression in lymph node (RPKM 27.7), spleen (RPKM 17.6) and 25 other tissues See more
Orthologs

Genomic context

See MBD4 in Genome Data Viewer
Location:
3q21.3
Exon count:
8
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 3 NC_000003.12 (129430944..129440179, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (129149787..129159022, complement)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene ribosomal protein L32 pseudogene 3 Neighboring gene small nucleolar RNA, H/ACA box 7B Neighboring gene EF-hand calcium binding domain 12 Neighboring gene intraflagellar transport 122 Neighboring gene rhodopsin enhancer region Neighboring gene rhodopsin

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Pathways from BioSystems

  • Base Excision Repair, organism-specific biosystem (from REACTOME)
    Base Excision Repair, organism-specific biosystemOf the three major pathways involved in the repair of nucleotide damage in DNA, base excision repair (BER) involves the greatest number of individual enzymatic activities. This is the consequence of ...
  • Base excision repair, organism-specific biosystem (from KEGG)
    Base excision repair, organism-specific biosystemBase excision repair (BER) is the predominant DNA damage repair pathway for the processing of small base lesions, derived from oxidation and alkylation damages. BER is normally defined as DNA repair ...
  • Base excision repair, conserved biosystem (from KEGG)
    Base excision repair, conserved biosystemBase excision repair (BER) is the predominant DNA damage repair pathway for the processing of small base lesions, derived from oxidation and alkylation damages. BER is normally defined as DNA repair ...
  • Base-Excision Repair, AP Site Formation, organism-specific biosystem (from REACTOME)
    Base-Excision Repair, AP Site Formation, organism-specific biosystemBase excision repair is initiated by DNA glycosylases that hydrolytically cleave the base-deoxyribose glycosyl bond of a damaged nucleotide residue, releasing the damaged base (Lindahl and Wood 1999,...
  • Cleavage of the damaged pyrimidine, organism-specific biosystem (from REACTOME)
    Cleavage of the damaged pyrimidine, organism-specific biosystemDamaged pyrimidines are cleaved by pyrimide-specific glycosylases (Lindahl and Wood 1999).
  • DNA Repair, organism-specific biosystem (from REACTOME)
    DNA Repair, organism-specific biosystemDNA repair is a phenomenal multi-enzyme, multi-pathway system required to ensure the integrity of the cellular genome. Living organisms are constantly exposed to harmful metabolic by-products, enviro...
  • Depyrimidination, organism-specific biosystem (from REACTOME)
    Depyrimidination, organism-specific biosystemDepyrimidination of a damaged nucleotide in DNA is mediated by a pyrimidine-specific DNA glycosylase. The glycosylase cleaves the N-C1' glycosidic bond between the damaged DNA base and the deoxyribos...
  • Displacement of DNA glycosylase by APEX1, organism-specific biosystem (from REACTOME)
    Displacement of DNA glycosylase by APEX1, organism-specific biosystemFollowing cleavage of the damaged base, DNA glycosylase is displaced by APEX1, an AP endonuclease (Parikh et al. 1998).
  • Recognition and association of DNA glycosylase with site containing an affected pyrimidine, organism-specific biosystem (from REACTOME)
    Recognition and association of DNA glycosylase with site containing an affected pyrimidine, organism-specific biosystemBase excision repair is initiated by a DNA glycosylase which first recognizes and removes a damaged or incorrect (e.g. mismatched) base (Sokhansanj et al. 2002).
  • Resolution of Abasic Sites (AP sites), organism-specific biosystem (from REACTOME)
    Resolution of Abasic Sites (AP sites), organism-specific biosystemResolution of AP sites can occur through the single nucleotide replacement pathway or through the multiple nucleotide patch replacement pathway, also known as the long-patch base excision repair (BER...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
DNA N-glycosylase activity TAS
Traceable Author Statement
more info
 
endodeoxyribonuclease activity TAS
Traceable Author Statement
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
pyrimidine-specific mismatch base pair DNA N-glycosylase activity IDA
Inferred from Direct Assay
more info
PubMed 
satellite DNA binding TAS
Traceable Author Statement
more info
PubMed 
Process Evidence Code Pubs
DNA repair TAS
Traceable Author Statement
more info
PubMed 
depyrimidination TAS
Traceable Author Statement
more info
 
response to estradiol IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
nuclear speck IDA
Inferred from Direct Assay
more info
 
nucleoplasm TAS
Traceable Author Statement
more info
 

General protein information

Preferred Names
methyl-CpG-binding domain protein 4
Names
3,N(4)-ethenocytosine glycosylase
G/5-fluorouracil mismatch glycosylase with biphasic kinetics
G/T mismatch glycosylase
G/U mismatch glycosylase
methyl-CpG binding domain protein 4
methyl-CpG-binding endonuclease 1
methyl-CpG-binding protein MBD4
mismatch-specific DNA N-glycosylase
putative methyl-CpG binding protein

NCBI Reference Sequences (RefSeq)

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_033106.1 RefSeqGene

    Range
    5001..14236
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001276270.1NP_001263199.1  methyl-CpG-binding domain protein 4 isoform 2

    See identical proteins and their annotated locations for NP_001263199.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) uses an alternate in-frame splice site in the 5' coding region, compared to variant 1. This results in a shorter protein (isoform 2), compared to isoform 1.
    Source sequence(s)
    BC011752, BP370521, BY997577, DB568237
    Consensus CDS
    CCDS63768.1
    UniProtKB/Swiss-Prot
    O95243
    Related
    ENSP00000394080.2, ENST00000429544.6
    Conserved Domains (2) summary
    smart00391
    Location:79155
    MBD; Methyl-CpG binding domain
    cl23768
    Location:444514
    ENDO3c; endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases
  2. NM_001276271.1NP_001263200.1  methyl-CpG-binding domain protein 4 isoform 3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) lacks an exon and its transcription extends past a splice site that is used in variant 1, resulting in a novel 3' coding region and 3' UTR compared to variant 1. It encodes isoform 3 which is shorter and has a distinct C-terminus, compared to isoform 1.
    Source sequence(s)
    AL449212
    Consensus CDS
    CCDS63766.1
    UniProtKB/Swiss-Prot
    O95243
    Related
    ENSP00000422327.1, ENST00000507208.1
    Conserved Domains (2) summary
    smart00391
    Location:79155
    MBD; Methyl-CpG binding domain
    cl23768
    Location:450520
    ENDO3c; endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases
  3. NM_001276272.1NP_001263201.1  methyl-CpG-binding domain protein 4 isoform 4

    See identical proteins and their annotated locations for NP_001263201.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) uses an alternate in-frame splice site in the 3' coding region, compared to variant 1. This results in a shorter protein (isoform 4), compared to isoform 1.
    Source sequence(s)
    AF532602, BP370521, BY997577, DB568237
    Consensus CDS
    CCDS63767.1
    UniProtKB/Swiss-Prot
    O95243
    Related
    ENSP00000424873.1, ENST00000503197.5
    Conserved Domains (2) summary
    smart00391
    Location:79155
    MBD; Methyl-CpG binding domain
    cl23768
    Location:450520
    ENDO3c; endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases
  4. NM_001276273.1NP_001263202.1  methyl-CpG-binding domain protein 4 isoform 5

    See identical proteins and their annotated locations for NP_001263202.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) uses an alternate in-frame splice site and lacks an exon in the 5' coding region, compared to variant 1. The encoded isoform (5) is shorter, compared to isoform 1.
    Source sequence(s)
    AM180876, BP370521, BY997577, CD678412, DB568237
    Consensus CDS
    CCDS63769.1
    UniProtKB/Swiss-Prot
    O95243
    Related
    ENSP00000376959.2, ENST00000393278.6
    Conserved Domains (1) summary
    cl23768
    Location:132202
    ENDO3c; endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases
  5. NM_003925.2NP_003916.1  methyl-CpG-binding domain protein 4 isoform 1

    See identical proteins and their annotated locations for NP_003916.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (1).
    Source sequence(s)
    AF072250, BP370521, BY997577, DB568237
    Consensus CDS
    CCDS3058.1
    UniProtKB/Swiss-Prot
    O95243
    Related
    ENSP00000249910.1, ENST00000249910.5
    Conserved Domains (2) summary
    smart00391
    Location:79155
    MBD; Methyl-CpG binding domain
    cl23768
    Location:450520
    ENDO3c; endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000003.12 Reference GRCh38.p12 Primary Assembly

    Range
    129430944..129440179 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_024453810.1XP_024309578.1  methyl-CpG-binding domain protein 4 isoform X1

    Conserved Domains (2) summary
    smart00391
    Location:79155
    MBD; Methyl-CpG binding domain
    cl27658
    Location:447512
    HHH; Helix-hairpin-helix motif
Support Center